DICOM @ OFFIS

Hi everyone, Just wanted to share that we have added Dicom image processing support in our highly scalable library for calculating features from intensity-label image data ( https://github.com/PolusAI/nyxus ). I want to thank the volunteers for helping me out with question regarding using DCMTK API....

Thanks!

Hi there,

My application only uses a select set of DCMTK modules: ofstd, oflog, dcmdata, dcmimgle, dcmimage, dcmjpeg, dcmjpls.

Is there a way to just build those (and preferably without the tests) using CMake?

Thanks,
Samee

Thanks for the reply. I did few more google search and what I understand is this behavior is due to the difference between how direct and indirect dependencies are resolved (at least in Linux). Here is a link that discusses this: https://stackoverflow.com/questions/52018092/how-to-set-rpath-and-runp...

Few updates. I reordered the link_directories() and add_executable() calls and the linking error is gone. However, now I get the following error: ./dicom_reader: error while loading shared libraries: liboflog.so.17: cannot open shared object file: No such file or directory using ldd shows the the fo...

I am getting a linking error like the following while trying to add DCMTK to my project. [100%] Linking CXX executable dicom_reader /usr/bin/ld: cannot find -lofstd /usr/bin/ld: cannot find -loflog /usr/bin/ld: cannot find -ldcmdata /usr/bin/ld: cannot find -li2d /usr/bin/ld: cannot find -ldcmimgle ...

Thanks for the reply.

I finally found that the package has been moved from the bioconda channel to conda-forge channel https://anaconda.org/conda-forge/dcmtk.

-Samee

Hi, Do the dcmtk developers/maintainers officially produce a conda package? I see that the bioconda channel has a dcmtk package https://anaconda.org/bioconda/dcmtk/ . But this is an old version (3.6.1), even though the tag says 3.6.7. Also, what is confusing is that the official bioconda page does n...

I think I have figured out the issue. I needed to register the codecs to be able to read the compressed image. Adding the following lines before everything seems to work. DJDecoderRegistration::registerCodecs(); DJLSDecoderRegistration::registerCodecs(); DcmRLEDecoderRegistration::registerCodecs();

Thanks for the reply. However, I still think something is wrong in my code. I picked another image from the pydicom-data repository (emri_small_jpeg_ls_lossless.dcm) which has the following properties. (0002, 0010) Transfer Syntax UID UI: JPEG-LS Lossless Image Compression (0002, 0012) Implementatio...

Yes, the image is compressed with JPEG200. Here is the tag value. Is there a way to find the list of the supported compressions for open source DCMTK?

Thanks,

Hello there. I am trying to use the DCMTK API to read some dicom files. The following piece of code works when the Pixel Representation value is 0 (uncompressed image, as I understand). However, when I am trying to read an image with pixel representation value 1, I get an error: Pixel representation...

Hi there, I am trying to read pixel data of a frame directly to an array. I looked at some example code from diinpxt.h file but not sure where I am making the mistake. I have the following code: auto dcm_ff = DcmFileFormat(); auto dcm_tag_pixel_data = DcmTagKey(0x7fe0,0x0010) ; dcm_ff.loadFile("/mnt...

Actually, I have found the issue. The UL type maps to "unsigned int" not "unsigned long". The following code works.

Hi there, I am working with a WSI Dicom image and I am trying to extract "Total Pixel Matrix Columns " tag's value. If I read the metadata and output it, I can see that this tag exists in the file. (0048, 0001) Imaged Volume Width FL: 9.72800064086914 (0048, 0002) Imaged Volume Height FL: 18.9440002...